In the food safety wiki question we recommend not keeping eggs at room temperature for more than 2-hours.
Eggs can sweat at room temperature and promote salmonella growth (which appears on the shell more often than inside). From USDA:
A cold egg left out at room temperature can sweat, facilitating the movement of bacteria into the egg and increasing the growth of bacteria. Refrigerated eggs should not be left out more than 2 hours.
From BC Centre for Disease Control:
Never leave cooked eggs or egg dishes at room temperature for longer than 2 hours.
and FDA requires egg refrigeration immediately and for retail. They also say:
SAFE HANDLING INSTRUCTIONS: To prevent illness from bacteria: keep eggs refrigerated, cook eggs until yolks are firm, and cook foods containing eggs thoroughly.
This literally means you shouldn't eat eggs sunny side up and plenty of restaurants serve them with regular eggs (you can pasteurize eggs with yolks remaining liquid).
The note about Refrigerated Eggs suggests that the USDA is aware that eggs keep at room temperature from the beginning may be safe. Most countries in the EU allow selling of eggs at room temperature. SA Answer: Howard McGee in "On Food & Cooking" says that egg quality deteriorates as much in one day at room temperature as it does four days under refrigeration. We were told the same thing in school.
The reason that eggs in the US are typically sold under refrigeration is because they are washed with warm water and detergent to remove the large amount of bacteria that are deposited on the shell while being layed. Once the cuticle is removed the egg becomes more porous.
What should be the recommendation then?